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- PDB-7cj2: Crystal structure of the Fab antibody complexed with human YKL-40 -

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Basic information

Entry
Database: PDB / ID: 7cj2
TitleCrystal structure of the Fab antibody complexed with human YKL-40
Components
  • Chitinase 3-like 1 (Cartilage glycoprotein-39), isoform CRA_a
  • Fab(Heavy chain)
  • Fab(Light chain)
KeywordsIMMUNE SYSTEM / Chitin binding protein / Inflammatory response / Fab / antibody-antigen complex / APOPTOSIS
Function / homology
Function and homology information


activation of NF-kappaB-inducing kinase activity / positive regulation of peptidyl-threonine phosphorylation / chitin binding / cellular response to interleukin-1 / positive regulation of interleukin-8 production / positive regulation of angiogenesis / cellular response to tumor necrosis factor / carbohydrate metabolic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / inflammatory response ...activation of NF-kappaB-inducing kinase activity / positive regulation of peptidyl-threonine phosphorylation / chitin binding / cellular response to interleukin-1 / positive regulation of interleukin-8 production / positive regulation of angiogenesis / cellular response to tumor necrosis factor / carbohydrate metabolic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / inflammatory response / apoptotic process / endoplasmic reticulum / extracellular space
Similarity search - Function
Chitinase-3-like protein 1 / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chitinase-3-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChoi, S. / Na, J.H. / Lee, S.J. / Woo, J.R. / Kim, D.Y. / Hong, J.T. / Lee, W.K.
CitationJournal: To Be Published
Title: Crystal structure of the Fab antibody complexed with human YKL-40
Authors: Choi, S. / Na, J.H. / Lee, S.J. / Woo, J.R. / Kim, D.Y. / Lee, W.K.
History
DepositionJul 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Fab(Heavy chain)
D: Fab(Light chain)
A: Chitinase 3-like 1 (Cartilage glycoprotein-39), isoform CRA_a
B: Chitinase 3-like 1 (Cartilage glycoprotein-39), isoform CRA_a
K: Fab(Heavy chain)
L: Fab(Light chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,1588
Polymers174,1476
Non-polymers1,0112
Water3,765209
1
C: Fab(Heavy chain)
D: Fab(Light chain)
A: Chitinase 3-like 1 (Cartilage glycoprotein-39), isoform CRA_a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6604
Polymers87,0743
Non-polymers5871
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-23 kcal/mol
Surface area30990 Å2
MethodPISA
2
B: Chitinase 3-like 1 (Cartilage glycoprotein-39), isoform CRA_a
K: Fab(Heavy chain)
L: Fab(Light chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4984
Polymers87,0743
Non-polymers4241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-24 kcal/mol
Surface area30370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.583, 132.526, 160.007
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Antibody , 2 types, 4 molecules CKDL

#1: Antibody Fab(Heavy chain)


Mass: 23128.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21[DE3]
#2: Antibody Fab(Light chain)


Mass: 23407.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21[DE3]

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Protein / Non-polymers , 2 types, 211 molecules AB

#3: Protein Chitinase 3-like 1 (Cartilage glycoprotein-39), isoform CRA_a


Mass: 40536.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHI3L1, hCG_24326 / Production host: Homo sapiens (human) / References: UniProt: A0A024R969
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 2 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 293.15 K / Method: microbatch / pH: 6.5
Details: 0.6M Sodium Chloride, 0.1M MES:NaOH, pH 6.5, 20% (w/v)PEG 4000, 1.0M NDSB-256

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.45→45.83 Å / Num. obs: 70738 / % possible obs: 99.84 % / Redundancy: 6.8 % / Biso Wilson estimate: 64.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.038 / Rrim(I) all: 0.1 / Net I/σ(I): 9.4
Reflection shellResolution: 2.45→2.48 Å / Rmerge(I) obs: 0.07466 / Num. unique obs: 70634 / CC1/2: 0.999 / CC star: 1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSv1.0.5data reduction
XDSv1.0.5data scaling
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HJX,5VEB

1hjx

5veb


Resolution: 2.7→45.83 Å / SU ML: 0.4011 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.0523
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2692 2640 4.98 %
Rwork0.2121 50356 -
obs0.2149 52996 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.62 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11441 0 67 209 11717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008511787
X-RAY DIFFRACTIONf_angle_d1.050416062
X-RAY DIFFRACTIONf_chiral_restr0.05381818
X-RAY DIFFRACTIONf_plane_restr0.00622058
X-RAY DIFFRACTIONf_dihedral_angle_d14.85851671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.750.38361410.29472601X-RAY DIFFRACTION99.93
2.75-2.80.35921360.27672619X-RAY DIFFRACTION99.86
2.8-2.860.34191440.25522609X-RAY DIFFRACTION100
2.86-2.920.32621190.24652623X-RAY DIFFRACTION99.89
2.92-2.990.33031440.25042595X-RAY DIFFRACTION100
2.99-3.060.32411500.24412619X-RAY DIFFRACTION99.89
3.06-3.150.31481410.23412637X-RAY DIFFRACTION100
3.15-3.240.3131460.2412595X-RAY DIFFRACTION99.85
3.24-3.340.27291360.22872645X-RAY DIFFRACTION99.96
3.34-3.460.24751450.212621X-RAY DIFFRACTION99.96
3.46-3.60.2481440.1982635X-RAY DIFFRACTION100
3.6-3.770.26571400.1972628X-RAY DIFFRACTION99.96
3.77-3.960.27891390.19242629X-RAY DIFFRACTION99.93
3.96-4.210.23641320.18232694X-RAY DIFFRACTION99.96
4.21-4.540.20871280.17642651X-RAY DIFFRACTION99.75
4.54-4.990.2291350.17332693X-RAY DIFFRACTION100
4.99-5.710.26011460.20282680X-RAY DIFFRACTION99.96
5.72-7.20.2891200.24842732X-RAY DIFFRACTION99.93
7.2-45.830.27441540.22732850X-RAY DIFFRACTION99.87

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